A smelly pile of empty shells buzzing with blowflies is the first step in an ambitious project to restore the lost reefs of the Pumicestone Passage in Queensland.

After several years of groundwork, Queensland's first oyster recycling project has begun accepting shells at the Ningi waste transfer station near Bribie Island.

Marine biologist Ben Diggles said the project would play a crucial role in re-establishing a once-thriving ecosystem.

"Today is a great day for us," Dr Diggles said.

"We're developing a modern midden by recycling oysters, diverting them from waste streams and converting them back to a useful product, which is raw material to rebuild shellfish reefs within Pumicestone Passage.

"Prior to European settlement there were many thousands of years of sustainable use by the Indigenous people here.

"When the first explorers arrived, those middens were mined and the shells were burnt to form lime to produce Brisbane's first buildings."

Exploitation, dredging and sediment run-off from land development destroyed the once-extensive shellfish reefs, but 100 years later the project involving community groups, Indigenous representatives and all levels of government has begun working to bring them back.

"Unfortunately today with the pressure that's on the Moreton Bay system and Pumicestone Passage in particular, it just needs a bit of help, it can't look after itself anymore," Dr Diggles said.

"Oysters link the energy in the system and turn it into fish and crabs, essentially into things we like to eat, and that just kickstarts that bottom end of the food chain, and we've seen that in small scale [reef restoration] trials.

"Without the oysters, that energy moves into things like algae and jellyfish, which are much less desirable.

"Sydney rock oysters filter between 2 to 4 litres of water an hour. You're talking nearly 100 litres of water a day per oyster, and so when you start getting them back in reefs in large numbers, it becomes quite a significant improvement in water quality."

Restaurants and a local supplier, Oysters on Bribie, have responded to the call for shell to recycle.

"I was actually quite surprised at how quickly we've developed this pile of oysters. We've only been going a few weeks and probably already got enough already for one of our trial reefs," Dr Diggles said.

He warned against people throwing seafood scraps direct into waterways.

"As always there's the right and wrong way to do things," he said.

"We separate the dirty and clean shell, dry them out in the sun and then we water blast them, get all the muck off them.

"After a period of four months they'll be ready to bag up and put back into the water.

"Essentially we set up the recycling centre so that the oysters are recycled the right way, and we're eliminating any biosecurity risks to the environment."

Moreton Bay Regional council has contributed $20,000 to the project, which has the support of mayor Allan Sutherland.

Leisha Krause, from the Joondoburri tribe, said Ningi was the Indigenous name for oyster.

"I think it's actually fantastic what they're trying to do. Years ago the passage was full of oysters," Ms Krause said.

Susie Chapman, from independent, not-for-profit organisation Healthy Land and Water, said she was working through the necessary applications with the State Government to place the first cleaned shells back in the Pumicestone Passage later this year.

"The primary purpose of this National Landcare-funded project is to improve fish habitat and bring back marine biodiversity," Ms Chapman said.